{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T02:37:35Z","timestamp":1775183855612,"version":"3.50.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2173,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Recent advances in single-cell manipulation technology, whole genome amplification and high-throughput sequencing have now made it possible to sequence the genome of an individual cell. The bioinformatic analysis of these genomes, however, is far more complicated than the analysis of those generated using traditional, culture-based methods. In order to simplify this analysis, we have developed SmashCell (Simple Metagenomics Analysis SHell-for sequences from single Cells). It is designed to automate the main steps in microbial genome analysis\u2014assembly, gene prediction, functional annotation\u2014in a way that allows parameter and algorithm exploration at each step in the process. It also manages the data created by these analyses and provides visualization methods for rapid analysis of the results.<\/jats:p>\n               <jats:p>Availability: The SmashCell source code and a comprehensive manual are available at http:\/\/asiago.stanford.edu\/SmashCell<\/jats:p>\n               <jats:p>Contact: \u00a0eoghanh@stanford.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq564","type":"journal-article","created":{"date-parts":[[2010,10,22]],"date-time":"2010-10-22T04:14:51Z","timestamp":1287720891000},"page":"2979-2980","source":"Crossref","is-referenced-by-count":23,"title":["SmashCell: a software framework for the analysis of single-cell amplified genome sequences"],"prefix":"10.1093","volume":"26","author":[{"given":"Eoghan D.","family":"Harrington","sequence":"first","affiliation":[{"name":"1 Department of Microbiology and Immunology, 2Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA, 3EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 4VIB - Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, 5Max Delbr\u00fcck Center for Molecular Medicine, D-13092 Berlin, Germany and 6Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA"},{"name":"1 Department of Microbiology and Immunology, 2Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA, 3EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 4VIB - Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, 5Max Delbr\u00fcck Center for Molecular Medicine, D-13092 Berlin, Germany and 6Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA"}]},{"given":"Manimozhiyan","family":"Arumugam","sequence":"additional","affiliation":[{"name":"1 Department of Microbiology and Immunology, 2Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA, 3EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 4VIB - Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, 5Max Delbr\u00fcck Center for Molecular Medicine, D-13092 Berlin, Germany and 6Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA"}]},{"given":"Jeroen","family":"Raes","sequence":"additional","affiliation":[{"name":"1 Department of Microbiology and Immunology, 2Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA, 3EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 4VIB - Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, 5Max Delbr\u00fcck Center for Molecular Medicine, D-13092 Berlin, Germany and 6Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA"}]},{"given":"Peer","family":"Bork","sequence":"additional","affiliation":[{"name":"1 Department of Microbiology and Immunology, 2Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA, 3EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 4VIB - Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, 5Max Delbr\u00fcck Center for Molecular Medicine, D-13092 Berlin, Germany and 6Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA"},{"name":"1 Department of Microbiology and Immunology, 2Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA, 3EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 4VIB - Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, 5Max Delbr\u00fcck Center for Molecular Medicine, D-13092 Berlin, Germany and 6Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA"}]},{"given":"David A.","family":"Relman","sequence":"additional","affiliation":[{"name":"1 Department of Microbiology and Immunology, 2Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA, 3EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 4VIB - Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, 5Max Delbr\u00fcck Center for Molecular Medicine, D-13092 Berlin, Germany and 6Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA"},{"name":"1 Department of Microbiology and Immunology, 2Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA, 3EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 4VIB - Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, 5Max Delbr\u00fcck Center for Molecular Medicine, D-13092 Berlin, Germany and 6Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA"},{"name":"1 Department of Microbiology and Immunology, 2Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA, 3EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 4VIB - Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, 5Max Delbr\u00fcck Center for Molecular Medicine, D-13092 Berlin, Germany and 6Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,10,21]]},"reference":[{"key":"2023012507525365900_B1","doi-asserted-by":"crossref","first-page":"2977","DOI":"10.1093\/bioinformatics\/btq536","article-title":"SmashCommunity: a metagenomic annotation and analysis tool","volume":"26","author":"Arumugam","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012507525365900_B2","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkn760","article-title":"STRING 8\u2013a global view on proteins and their functional interactions in 630 organisms","volume":"37","author":"Jensen","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012507525365900_B3","doi-asserted-by":"crossref","first-page":"11889","DOI":"10.1073\/pnas.0704662104","article-title":"Dissecting biological \u201cdark matter\u201d with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth","volume":"104","author":"Marcy","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012507525365900_B4","doi-asserted-by":"crossref","first-page":"e5299","DOI":"10.1371\/journal.pone.0005299","article-title":"Assembling the marine metagenome, one cell at a time","volume":"4","author":"Woyke","year":"2009","journal-title":"PloS ONE"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/23\/2979\/48851330\/bioinformatics_26_23_2979.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/23\/2979\/48851330\/bioinformatics_26_23_2979.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T07:53:13Z","timestamp":1674633193000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/23\/2979\/220945"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,10,21]]},"references-count":4,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2010,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq564","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,12,1]]},"published":{"date-parts":[[2010,10,21]]}}}